title: Identification of genes associated with the onset of colorectal cancer by transcriptomic analyses of the adenoma-carcinoma sequence

status: Public on Aug 31 2021

city: shanghai

first: HONG

last: QIN

address: 130# Dongan road

country: China

institute: Fudan Univercity

type: Expression profiling by high throughput sequencing

summary: In the carcinogenesis of colorectal cancer (CRC), the stepwise progression from adenoma to carcinoma is marked by a series of specific genetic alterations of known oncogenes and tumor suppressor genes. However, many patient-matched features of the transcriptome involved in the adenoma-carcinoma sequence remain unidentified. The aim of this study was to identify genes associated with the process of CRC formation by analyzing the characteristics of the transcriptome during tumor formation. Six dynamic expression patterns specific to tumor formation were characterized for the first time. Dysregulation of metabolic pathways, suppression of the immune system, and activation of canonical pathways related to cancer were associated with the adenoma-carcinoma sequence. Among a cluster of genes positively correlated with tumor formation, TPD52L1 was identified as a gene that induced oncologic behaviors and a biomarker for poor prognosis.

overall_design: Triplicate tissue samples (primary CRC, adjacent normal tissue, and adenoma; n = 15) were collected from five patients with CRC prior to any therapy at Zhongshan Hospital, and stored in RNAlater™ Stabilization Solution.Total RNA samples were extracted with the TRIzol™ Reagent (Thermo Fisher Scientific). Ribosomal-RNA-depleted and strand-specific libraries were constructed with the Ribo-Zero Gold Kit (Illumina, Inc., San Diego, CA, USA) and TruSeq Stranded Total RNA Sample Prep Kit (Illumina, Inc.), and sequenced using the HiSeq 2500 Sequencing System (Illumina, Inc.) by Genergy BioTech Co., Ltd. (Delhi, India). Cleaned RNAseq data were aligned to the human GRCh38 reference assembly using the HISAT2 alignment program [50]. Only uniquely mapped reads were retained for reads counting with HTseq [51]. DEGs were identified with the R package DESeq2 [52]. To identify the DEGs between two tissue specimens in different transitional stages, the Wald test in DESeq2 was applied with a false discovery rate (FDR) of <0.05 and absolute log2 (fold change) of >1. To identify DEGs in all three tissue types, the likelihood-ratio test (LRT) was used with an FDR threshold of <0.05.

first: Qin

last: Hong

first: Bing

last: Li

first: Yunshi

last: Zhong

first: Bo

last: Wen


title: Comparative Transcriptomics on cellular reactions to short-term hypergravity [RNA-Seq]

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

summary: Jurkat T cells have been lysed after exposure to 15 minutes of 9g in a ground-based pipette centrifuge. The RNA samples were parallely analyzed with RNA-Seq and microarray transcriptomics.

overall_design: 1 hypergravity condition (9g, 15 minutes). 1 ground control condition with exact same setup including aspiration of cells into pipettes and lysis after 15 minutes, but without hypergravity. 4 samples per condition.

first: Christian

last: Vahlensieck

first: Oliver

last: Ullrich


title: Dynamics of global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain

city: Little Rock

first: Kimberly

middle: E

last: Stephens

state: AR

address: 4301 W. Markham St Slot 510

department: Neuroscience

country: USA

institute: University of Arkansas for Medical Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Shared transcriptomic and epigenetic changes in two animal models improves our understanding of how chromatin structural changes alter dorsal root ganglion (DRG) gene expression under persistent pain conditions.

overall_design: Examination of gene expression and chromatin accessibility in naïve and injured, male rats.


title: A SIX6 reporter for studies of early optic development

city: La Jolla

first: Karl

last: Wahlin

state: CA

address: 9415 Campus Point Dr., #0946

department: Ophthalmology

institute: UC San Diego

summary: Human pluripotent stem cells represent an exciting tool to investigate the mechanisms of human eye development and to build human models of retinal dystrophy. To explore the dynamics of early eye development in a carefully controlled setting and optimize this process, we have developed an eyefield expressed SIX6-GFP reporter that enables the systematic optimization of early eye-field development allowing the identification of conditions that favor early optic development.

overall_design: Pooled day 65 retina cups (n>3/sample) were separated as either GFP- (n=4), GFP+ (n=4) or SIX6+/POU4F2+ (n=4) samples (total of 12 samples run for RNA-seq).

first: Shawna

last: Jurlina

first: Melissa

last: Jones

first: Jie

last: Cheng

first: Nawal

last: Kibria

first: Anna

last: Ogata

first: Kiara

last: Eldred

first: Sunayan

last: Ray

first: Catherine

last: Kim

first: Jacob

last: Heng

first: Robert

last: Johnston

first: Jenny

last: Phillips

first: David

last: Gamm

first: Cindy

last: Berlinicke

first: Donald

last: Zack


title: Next-generation sequencing facilitates quantitative analysis of transcriptomes of pro-inflammatory cytokines stimulated mouse dorsal root ganglionic neurons infected with lentivirus expressing GFP or a SNAP-25 cleaving protease

city: Dublin

first: Jiafu

last: Wang

address: Collins Avenue,, Glasnevin

country: Ireland

institute: Dublin City University

summary:
Purpose: The goals of this study are to investigate the influence of viral mediated cleavage of SNAP-25 in mouse dorsal root ganglionic neurons (mDRGs) on transcriptome profiling (RNA-seq).
Methods: A total of 6 samples were tested using the DNBSEQ platform, 3 samples with viral mediated expression of GFP in mDRGs, the other 3 samples with viral mediated expression of the light chain protease of botulinum toxin A (LCA) in mDRGs, with an average yield of 1.12 G data per sample. The average alignment ratio of the sample comparison genome was 96.00%, which was comparative. The average alignment of the gene set was 83.78%; a total of 19963 genes were detected.
Results: Using an optimized data analysis workflow, RNA-seq data confirmed cleavage of SNAP-25 affects the mRNA levels of certain neuropeptide genes, receptors and transducers. Altered expression of 5 genes were validated using RT–qPCR. RNA-seq data were consistent with RT-qPCR, demonstrating the high degree of sensitivity of the RNA-seq method.
Conclusions: Our study show that viral mediated cleavage of SNAP-25 robustly downregulated mRNA levels of certain neuropeptide genes, receptors and transducers.

overall_design: A total of 6 samples were tested using the DNBSEQ platform, 3 samples with viral mediated GFP expression in mDRGs and the other 3 with viral mediated expression of LCA.

first: Wanzhi


title: The tetratricopeptide repeat and J-domain containing proteins DJC31 and DJC62 are involved in abiotic stress response in Arabidopsis thaliana

status: Public on Aug 30 2021

city: Planegg-Martinsried

first: Serena

last: Schwenkert

address: Grosshadernerstr. 2-4

department: Biology

country: Germany

institute: LMU

type: Non-coding RNA profiling by high throughput sequencing

summary: Molecular chaperones play an important role during the response to different stresses. Since plants are sessile organisms, they need to be able to adapt quickly to different conditions. To do so, plants possess a complex chaperone machinery, composed of HSP70, HSP90, J-proteins and other factors. In this study we characterized DJC31 and DJC62, two J-proteins that additionally carry clamp type tetratricopeptide repeat (TPR) domains. Using cell fractionation and self-assembly GFP, we could show that both proteins are attached to the cytosolic side of the endoplasmic reticulum membrane. Moreover, an interaction with cytosolic HSP70 and HSP90 could be shown by bimolecular fluorescence complementation. Knockout of either DJC31 or DJC62 caused only a mild phenotype, which is overall comparable to wild type. However, the double mutant exhibited severe defects in growth and development, which affected almost all organs. Furthermore, it could be shown that the double mutant is more sensitive to osmotic stress and treatment with abscisic acid, but surprisingly exhibited enhanced tolerance to drought. Taken together, these findings indicate that DJC31 and DJC62 might be acting as important regulators of chaperone dependent signalling pathways involved in plant development and stress response.

overall_design: Examination of differential gene expression in the Arabdidopsis thaliana djc mutants compared to wild type in three replicates


title: Transcriptome analysis of Sertoli cells in Equus asinus

city: Qingdao

first: JunLin

last: Song

address: Changcheng Road

institute: JunLin Song

summary: Deoxynivalenol (DON) and zearalenone (ZEA) are the most common mycotoxins, which are damaging to the reproductive system of humans and animals. Sertoli cells perform vital roles of male reproduction include composition of the blood testis barrier, support and release sperm. In the present study, transcriptomic analysis was conducted on different dosages (0 μM, 10 μM and 30 μM) of DON and ZEA treated donkey Sertoli cells. Transcriptomic analysis showed 6551 differentially expressed genes (DEGs) were identified between DON 10 μM treatment group and control group, with 3300 up regulated and 3251 down; 8605 DEGs were identified between DON 30 μM treatment group and control group, with 4841 up regulated and 3764 down; 803 DEGs were identified between ZEA 10 μM treatment group and control group, with 391 up regulated and 412 down; and 5947 DEGs were identified between ZEA 30 μM treatment group and control group, with 2816 up regulated and 3131 down. In DEGs, Caspase-1, GSDMD-NT, ESR 1, AR, PRDX 4, NOX 1, MSH 6 and CDK 1, were expressed highly in DON and ZEA treatment group, which related to pyroptosis, hormone secretion, oxidative stress and cancerous. It is unprecedented that DON induced cell death by pyroptosis. This study provides valuable genetic resources for understanding the mechanisms and pathways of the toxin effect of DON and ZEA for Equus asinus' Sertoli cells.

overall_design: Total mRNA profiles of DON and ZEA treated Sertoli cells were generated by deep sequencing, in triplicate.

first: Guoliang

last: Zhang


title: Comparative study of effect of thalidomide, lenalidomide and pomalidomide on Human umbilical vein endothelial cells (HUVECs)

city: Madras Institute of Technology, Chrompet

first: Suvro

last: Chatterjee

state: Tamil Nadu

address: Vascular Biology Laboratory

country: India

institute: AU-KBC Research Centre, Anna University

summary: Scope: To compare the anti angiogenic potential of thalidomide with its analogs

overall_design: The trancriptome sequencing was performed using Illumina HiSeq 2500 ® platform.The sequence reads were aligned with  Homosapiens genome downloaded from Ensembl release 75 database. Alignment of sequence were performed using STAR program (version 2.5.1b) program with Homosapiens gene model with default parameter settings.cuffdiff(v2.2.0) program was used to perform differential expression gene analysis.Heat maps were generated for gene expression analysis using R statistical software 3.1.0. Pathway analysis were performed to investigate differential gene expression analysis using DAVID program.

first: Pavitra

last: Kumar

first: Akila

middle: S

last: Swaminathan

first: Ravi

last: Gupta


title: Localized inflammation mediators in a murine acute mastitis model

city: Burlington

first: Feng-Qi

last: Zhao

state: VT

address: #211 Terrill Building, 570 Main Street

department: Department of Animal and Veterinary Sciences

institute: University of Vermont

summary: We report the transcriptome changes in mouse mammary gland locally treated with lipopolysacchride (LPS) for 12 h.

overall_design: The left and right sides of the 4th pair of mouse mammary glands were alternatively injected with either lipopolysaccharide (LPS, E. coli 055: B5, 50 μL of 0.4 mg/mL) or sterile PBS through the teat meatus 3 days postpartum (n = 9). The 4th glands were individually collected at 12 h after the LPS injection and analyzed for gene expression changes by RNA sequencing

first: Miyuki

last: Takashima


title: Single-cell analysis identifies shared and distinct immune features of COVID-19, Influenza and other community-acquired pneumonia

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

summary: The exact immunopathophysiology of COVID-19 remains clouded by methodological heterogeneity and a lack of relevant disease controls. The absence of single-cell investigations into the broader population of patients with community-acquired pneumonia (CAP) renders it difficult to distinguish immune features unique to COVID-19 from the common characteristics of a dysregulated host response to pneumonia. We performed integrated single-cell transcriptomic and proteomic analyses in PBMCs from a strictly matched cohort of eight patients with COVID-19, eight patients with CAP, and four non-infectious control subjects. With this balanced, multi-omic approach we describe diverging transcriptional and phenotypic patterns in T cell, NK cell and monocyte populations between patients with CAP caused by either SARS-CoV-2, Influenza A or other pathogens, and thereby expand our understanding of the peripheral immune response in different forms of CAP.

overall_design: Single-cell transcriptomic and proteomic analysis of PBMCs from eight COVID-19 patients, 8 CAP patients (3 CAP-Flu) and 4 matched controls. Comparisons: COVID-19 vs controls, CAP vs controls, COVID-19 vs CAP.

first: Alex

middle: R

last: Schuurman

first: Tom

middle: D

last: Reijnders

first: A

last: Saris

first: Ivan

last: Moral

first: M

last: Schinkel

first: C

last: van Linge

first: L

last: Vermeulen

middle: P

first: W

middle: J

last: Wiersinga

first: Felipe

middle: A

last: Vieira Brage

last: van der Poll


title: miRNA profiling of plasma from FMR1 premutation carriers

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

summary: Abnormal trinucleotide expansions cause rare disorders that compromise quality of life and, in some cases, life span. In particular, the expansions of the CGG-repeats stretch at the 5'-UTR of the Fragile X Mental Retardation 1 (FMR1) gene have pleiotropic effects that lead to a variety of Fragile X-associated syndromes: the neurodevelopmental Fragile X syndrome (FXS) in children, the late-onset neurodegenerative disorder Fragile X-associated tremor-ataxia syndrome (FXTAS) that mainly affects adult men, the Fragile X-associated primary ovarian insufficiency (FXPOI) in adult women, and a variety of psychiatric and affective disorders that are under the term of Fragile X-associated neuropsychiatric disorders (FXAND). There have been intensive attempts to identify reliable peripheral biomarkers to assess disease progression and onset of specific pathological traits. We profiled the miRNAs content of plasma from premutation carriers and controls. Understanding the association between molecular pathogenesis and biomarkers dynamics will improve effective prognosis and clinical management of CGG-expansion carriers

overall_design: Comparison between premutation carriers and control donors


title: Fibro-Adipogenic muscle Progenitors (FAP) and myogenic progenitors (MPs) display a distinct miRNA expression profile that is modulated in response to TGFβ1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Fibrosis is a deleterious invasion of tissues associated with many pathological conditions, such as Duchenne muscular dystrophy (DMD) for which no cure is at present available for its prevention or its treatment. Fibro-adipogenic progenitors (FAPs) are resident cells in the human skeletal muscle and can differentiate into myofibroblasts, which represent the key cell population responsible for fibrosis. In this study, we delineated the pool of microRNAs (miRNAs) that are specifically modulated by TGFβ1 in FAPs versus myogenic progenitors (MPs) by a global miRNome analysis. A subset of candidates, including several "FibromiRs", was found differentially expressed between FAPs and MPs and was also deregulated in DMD versus healthy biopsies. Among them, the expression of the TGFβ1-induced miR-199a~214 cluster was strongly correlated with the fibrotic score in DMD biopsies. Loss-of-function experiments in FAPs indicated that a miR-214-3p inhibitor efficiently blocked expression of fibrogenic markers in both basal conditions and following TGFβ1 stimulation. We found that FGFR1 is a functional target of miR-214-3p, preventing the signaling of the anti-fibrotic FGF2 pathway during FAP fibrogenesis. Overall, our work demonstrates that the « FibromiR » miR-214-3p is a key activator of FAP fibrogenesis by modulating the FGF2/FGFR1/TGFβ axis, opening new avenues for the treatment of DMD.

overall_design:
Small RNA-seq of FAPs and MPs from three muscle biopsies treated or not by TGFβ1 was performed and showed that FAPs and MPs expressed very different subsets of miRNAs. A subset of 59 miRNAs efficiently discriminated FAPs- and MPs-derived samples. Moreover, additional miRNAs were differentially regulated by TGFβ1, pointing out a specific miRNome modulation in the 2 muscle cell progenitors during differentiation.
FAPs and MPs from three healthy skeletal muscles were treated or not with 5 ng/mL TGFβ1 for 48h, total RNA was purified and subjected to Small RNA-seq, for a total of 12 distinct samples

first: K

first: B

last: Mari

last: Dani

first: P

last: Barbry


title: Characterization of Entamoeba histolytica adapted to auranofin by combined transcriptomics and redox proteomics

city: Haifa

first: Serge

last: Ankri

address: Efron 1

country: Israel

institute: Technion

summary:
Purpose: Transcriptome characterization of Entamoeba histolytica trophozoites adapted to Auranofin
Total RNA was extracted from control trophozoites (WT) and AFAT using the TRI reagent kit, according to the manufacturer instructions (Sigma-Aldrich USA).   6 RNAseq libraries were produced according to manufacturer protocol (NEBNext UltraII Directional  RNA Library Prep Kit for Illumina, cat no. E7760) using 800ng total RNA. mRNAs pull-up was performed using Magnetic Isolation Module (NEB, cat no. E7490). All libraries were mixed into a single tube with equal molarity. The RNAseq data was generated on Illumina NextSeq500, 75 single-end read, high output mode (Illumina, cat no. 200249)  The number of reads per gene was counted using Htseq-count (v0.9.1)
Results: Transcriptomics of Entamoeba histolytica trophozoites that were adapted to 2 uM Auranofin revealed an upregulation of genes encoding cytoskeletal proteins, dehydrogenases and guanyl-nucleotide exchange factors.
Conclusions: Adaptation to Auranofin comes with a fitness cost for E.histolytica that includes a decreased growth rate and virulence and  sensitivity to Oxidative stress, Nitrosative stress and to Metronidazole. Overexpression of genes whose products are sensitive to Auranofin-mediated oxidation may represent an important step in the adaptation process to Auranofin and EhTrxR does not seem to be central for this process.

overall_design: Entamoeba histolytica mRNA profiles of WT and Auranofin adapted (2uM) trophozoites

first: Yana

last: Shaulov

first: Lotem

last: Sarid

first: Meirav

last: Trebicz-Geffen


title: Identification of genes related to male sterile in Prunus sibirica

city: Shenyang

first: Jianhua

last: Chen

state: Liaoning

address: No.120 Dongling Road, Shenhe District

institute: Shenyang Agricultural University

summary: Stamen development is an important developmental process that directly affects the yield of Prunus sibirica. In this study, the male sterile flower buds and male fertile flower buds of Prunus sibirica were used as materials to performed RNA-Seq analyses to compare transcription differences. The results would provide a theoretical basis for further investigation of the formation mechanism of male sterile flower.

overall_design: Male sterile flower buds of clone No. 1 were selected as the experimental group, and male fertile flower buds of clone No. 60 were selected as the control group. Flower bud samples of male sterile clone and male fertile clone were collected from the end of July in 2018 to the beginning of April in 2019. Samples were taken every 10 to 15 days. Every time 10~20 complete flower buds without diseases and insect pests were selected from the upper part of the fruiting branches outside the canopy on the sunny side, which were collected and quickly stored in FAA fixative for making paraffin sections of flower buds. At the same time, three biological replicates of flower buds were collected and rapidly plunged into the liquid nitrogen (-196℃). The samples were taken back to the laboratory and stored in an ultra-low temperature freezer(-80°C). Total RNA was extracted from male sterile flower buds and fertile flower buds by RNA extraction kit of Tiangen Biotech (Beijing) Co., Ltd. The RNA librarie sequencing based on Illumina HiSeq platform by paired-end experiments.

first: Sheng

last: Dong

first: Jian

middle: H

first: Quan

middle: G

last: Liu


title: Endometriosis and Pain samples

city: Guildford

first: Fernando

middle: O

last: Martinez Estrada

state: Surrey

address: Stag Hill

department: Faculty of Health & Medical Sciences

country: United Kingdom

institute: University of Surrey

summary: We focus on the characterization of gene expression profiles in circulating monocytes and peritoneal fluid Mononuclear phagocytes in patients with endometriosis

overall_design:
Examination of differences between women with pain and women with diagnosed endometriosis.
>>> Submitter declares that the raw data are unavailable due to patient privacy concerns. <<<

first: Udo

last: Oppermann


title: Human T-cell dysfunction induced in repeatedly stimulated cultures.

city: Montreal

first: Jean-Sebastien

last: Delisle

state: Quebec

address: 5415 Boulevard de l'Assomption

country: Canada

institute: Centre de recherche de l'Hôpital Maisonneuve-Rosemont

summary: We report the changes in mRNA profile of quiescent, activated and dysfunctional human CD8+ T cells in culture according to a protocol of weekly polyclonal stimulations relevant to immunotherapy.

overall_design: mRNA profile of quiescent enriched CD8+ T cells compared to cells after one stimulation with anti-CD3/CD38 beads or 5 to 7 rounds of weekly stimulations.

first: Valérie

last: Janelle

first: Jean-Sébastien


title: Small RNA Seq of DMD muscle biopsies identifies a miRNA signature associated with fibrotic status

first: Kevin

overall_design:
Eight DMD muscle biopsies and 3 age-matching control muscle biopsies were selected on the basis of their fibrosis status. RNA samples were extracted from biopsies and subjected to small-RNA-seq.
Small RNA libraries from the 11 samples were multiplexed and sequenced on an Applied Biosystems SOLiD 5500 wildfire system

first: C


title: DNMT3B-mediated DNA methylation and silencing of OCT1-targeted oncogenes in response to pterostilbene

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

institute: The University of British Columbia

summary: Transcription factor (TF)-mediated regulation of genes is often disrupted during carcinogenesis. The DNA methylation state of TF-binding sites may dictate transcriptional activity of corresponding genes. Stilbenoid polyphenols, such as pterostilbene (PTS), have been shown to exert anti-cancer action by remodeling DNA methylation and gene expression patterns of tumor suppressor genes and oncogenes. However, the mechanisms behind these effects still remain unclear. Here, the dynamics between oncogenic TF, OCT1, binding and de novo DNA methyltransferase, DNMT3B, binding in PTS-treated MCF10CA1a invasive breast cancer cells has been explored. Using chromatin immunoprecipitation (ChIP) followed by next generation sequencing, we determined 47 gene regulatory regions with decreased OCT1 binding and enriched DNMT3B binding in response to PTS. Most of those genes were found to have oncogenic and pro-metastatic functions. PRKCA, a gene encoding for protein kinase C alpha (PKC-alpha), was selected for further mechanistic investigation due to its functional and regulatory connection with numerous oncogenic pathways and cancer-driving processes. Two additional genes, troponin T2 (TNNT2) and DXZ4 associated non-coding transcript 2 (DANT2), were also investigated as they demonstrated some of the highest increase in DNMT3B occupancy and novel oncogenic functions. PTS led to the recruitment of DNMT3B to the PRKCA promoter region and TNNT2 and DANT2 enhancers at loci that are occupied by OCT1 in vehicle-treated cells. Substantial decrease in OCT1 occupancy with increased DNMT3B binding were accompanied by PRKCA promoter and TNNT2 and DANT2 enhancer hypermethylation, and gene silencing. Interestingly, hypermethylation of the regulatory regions of the genes in response to PTS was not detected in DNMT3B-CRISPR knockout MCF10CA1a breast cancer cells, which indicates DNMT3B-dependent methylation of PRKCA, TNNT2, and DANT2 upon PTS treatment. Our findings provide a better understanding of mechanistic players and their gene targets that possibly contribute to the anti-cancer action of stilbenoid polyphenols.

overall_design: Examination of occupancy of DNMT3B and OCT1 in MCF10CA1a breast cancer cells after treatment with pterostilbene (PTS).

first: Megan

last: Beetch

first: Cayla

last: Boycott

first: Sadaf

last: Harandi-Zadeh

first: Tony

last: Yang

first: Benjamin

last: Martin

first: Thomas

last: Dixon-McDougall

last: Ren

first: Allison

last: Gacad

first: John

last: Dupuis

first: Katarzyna

last: Lubecka

first: Rickey

middle: Y

last: Yada

first: Carolyn

last: Brown

first: LeAnn

last: Howe


title: NF-κB1 (p50) impairs macrophage driven inflammatory response of the host against Helicobacter pylori infection

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

summary: In the present study, we observed spontaneous gastritis in 10-12 week old NF-κB1—/— mice with increased level of pro-inflammatory cytokines in gastric tissues. The NF-κB1—/— bone marrow derived macrophages showed increased level of cytokines which further exacerbated with H. pylori infection. To map the contribution of macrophages in the spontaneous gastritis, we performed comparative transcriptome analysis of NF-κB1—/— mice gastric macrophage and H. pylori treated macrophages. The transcriptome analysis showed an upregulation of innate immune response genes in NF-κB1—/— gastric macrophages, but not in H. pylori activated murine macrophages. Network analysis identified STAT1/TLR7/TLR13 as a key regulator and inhibition of STAT1 activation attenuated exacerbated innate immune response. NF-κB1—/— mice after infection with H. pylori showed increased histological gastritis and reduced level of H. pylori colonization. Our study indicates that H. pylori-mediated up-regulation of NF-κB1 mitigates host immune response and promotes chronic colonization of the pathogen.

overall_design: Comparative RNA profiles of H. pylori ex-vivo activated mice gastric macrophages and  NF-κB1 knock-out/wild type mice gastric macrophages

first: Shilpi

last: Gupta

first: Kalaiarasan

last: Ponnusamy

first: Jyoti

first: Rohit

last: Tiwari

first: Achyut

last: Pandey

first: Rajesh

last: Kumari

first: Maya

last: Chaturvedi

first: Ashwini

last: Kumar Ray

first: Surabhi

last: Kirti Mishra

first: Ravi

last: Tandon

first: Pawan

last: Kumar Dhar

first: Rupesh


title: RNA-seq profiling of cultured B16 F0, F1 and F10 cells

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

institute: University of British Columbia

summary: To contrast and compare the transcriptomes of poorly metastatic B16 sub-clones F0 and F1 to the highly metastatic sub-clone F10.

overall_design: Transcriptome wide profiling of in vitro cultured B16 lines F0, F1 and F10

first: K

last: Wiegand

first: T


title: Transcriptome profile of Brassica napus seed development

city: Winnipeg

first: Mark

last: Belmonte

state: Manitoba

address: 50 Sifton Rd

department: Biological Sciences

institute: University of Manitoba

summary: We profiled the gene regulatory landscape of Brassica napus reproductive development using RNA sequencing. Comparative analysis of this nascent allotetraploid across the plant lifecycle revealed the contribution of each subgenome to plant reproduction. Global mRNA profiling across reproductive development revealed lower accumulation of C subgenome transcripts relative to the A subgenome. Subgenome-specific transcriptional networks identified distinct transcription factor families enriched in each of the A and C subgenome in early seed development. Analysis of a tissue specific transcriptome of early seed development revealed transcription factors predicted to be regulators encoded by the A subgenome are expressed primarily in the seed coat whereas regulators encoded by the C subgenome were expressed primarily in the embryo. Whole genome transcription factor networks identified BZIP11 as an essential regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in knockdown of predicted target genes, and a reproductive-lethal phenotype. Our data indicate that subgenome bias are characteristic features of the B. napus seed throughout its development, and that such bias might not be universal across the embryo, endosperm, and seed coat of the developing seed. We also find that examining transcriptional networks spanning both the A and C genomes of the whole B. napus seed can identify valuable targets for seed development research. We suggest that-omics level approaches to studying gene regulation in B. napus can benefit from both broad and high-resolution analyses.

overall_design: RNA were isolated from ovules, and seeds 7 (GLOB), 10 (HEART), 28 (MG), and 35 (DS) days post fertilization. Three replicates were sequenced for each stage except DS, for which only 2 replicates were sequenced. Samples were sequenced 100bp SE reads on the Illumina HiSeq2500. Reads were trimmed with Trimmomatic 0.36 and aligned with HiSat2 to the DH12075 genome. Counts, normalization, and differential expression were called using Cuffquant and Cuffdiff.

first: Deirdre

last: Khan

middle: F

first: Isobel

last: Parkin

first: Steven

last: Robinson


title: Transcriptional analysis of anole lungs at E18

city: Princeton

first: Michael

middle: A.

last: Palmer

state: New Jersey

address: 25 William Street

department: Chemical and Biological Engineering

institute: Princeton University

summary: This project aims to establish the embryonic anole lung as a model for investigating lung development and more general epithelial morphogenesis by generating a set of single-cell RNA-seq (scRNA-seq) data from late-stage embryonic lungs taken from brown anoles (Anolis sagrei). The anole lung, with its simple architecture, provides a novel tool for investigating signaling in a less complex respiratory system than the murine lung, and this data set would be a large advance in making this system more widely known and accesible among developmental biologists.

overall_design: Lungs were dissected from anole embryos at embryonic day 18 and dissociated in dispase. Cells were processed in the 10x Genomics Chromium system. The tissues we isolated contain all expected cell types of embryonic lungs, including mesenchymal cells at each stage of differentiation into smooth muscle.

first: Celeste

last: Nelson


title: The potential biomarkers for HCC patients with functional loss of both p53 and Tsc1

city: Chongqing

first: Chuanming

last: Xie

state: Chongqing

address: 30 Gaotanyan Rd

department: Institute of Hepatobiliary Surgery

institute: Southwest Hospital

summary: p53 mutations occur frequently in human hepatocellular carcinoma (HCC). Activation of the mammalian target of rapamycin (mTOR) pathway is also associated with HCC. However, it is still unknown whether these changes together initiate HCC and can be targeted as a potential therapeutic strategy.  Here, we compared transcriptional profiles among a panel of liver tissue samples from p53+/-, Tsc1fl/fl;Alb-cre, and p53+/-;Tsc1fl/fl;Alb-cre mice by RNAseq analysis. The overlapping genes in those three genotypes were considered potential biomarkers for HCC patients with functional loss of both p53 and Tsc1.

overall_design: Transcriptome analysis was performed in p53 loss and Tsc1 loss liver tissues isolated from 320 days mice (6 groups, n=3 per group).

first: Chuan-Ming


title: Identification of the AdcR-regulated genes in Streptococcus suis by RNA sequencing analysis.

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

institute: Yangzhou University

summary: RNA sequencing analysis of the transcriptome of the wild type (WT) strain and ΔadcR mutant. The data revealed that genes encoding the Zn acquisition systems were negatively regulated by AdcR.

overall_design: The WT and ΔadcR strains were cultured in Tryptic Soy Broth supplemented with 10% (vol/vol) newborn bovine serum (TSBS) and grown to mid-exponential phase (OD600 = 0.6). Total RNA was isolated and subjected to RNA sequencing analysis. Biological triplicate samples obtained from three independent experiments were used.

first: Jun

last: Qiu

first: Man

last: Wei


title: Transcriptomic profiling of subcutaneous white adipose tissue with selective ablation of Bmal1 at ambient and cold condition

city: Duarte

first: Ke

last: Ma

address: 1500 E. Duarte Rd

department: Diabetes Complications & Metabolism

institute: City of Hope-BRI

summary: Mice with beige fat-selective ablation of Bmal1 were generated by crossing Bmal1fl/fl with Prrx1-Cre transgenics. Inguinal subcutaneous adipsoe tissues were collected under ambient temperature at 220C or  cold acclimations at 10oC for two weeks.

overall_design: RNA-seq analysis of the subcutaneous fat inguinal white adipose tissue (iWAT) in both ambient(22oC) and cold(10oC) conditions for the BMCtr and BMKO groups.

first: Xuekai

last: Xiong

first: Xiwei

last: Wu

first: Charles

last: Warden


title: Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID

city: London

first: Dimitris

last: Katsanos

address: Sir Alexander Fleming building, Imperial College Road

department: Life Sciences

institute: Imperial College London

summary: In this study we use targeted DamID to assay RNA polymerase occupancy across the genome specifically within the seam cells and hypodermis of C. elegans to identify genes expressed in these cell-types.

overall_design: Identification of sets of expressed genes within the seam cells and the hypodermis of C. elegans by cell-type-specific expression of a DAM:RPB-6 fusion using the seam cell promoter srf-3i1 and the hypodermal promoter dpy-7syn1. DAM:RPB-6 occupancy across the genome is assayed in the form of GATC 6mA methylation in comparison to that of an equivalent control DAM:NLS-GFP fusion and genes with significant levels of occupancy are identified. Two biological replicates were aquired for every fusion and cell-type at each of the L2 and L4 developmental stages.

first: Michalis

last: Barkoulas


title: The FibromiR miR-214-3p is upregulated in fibrotic Duchenne Muscular Dystrophy and promotes differentiation of Fibro-Adipogenic muscle progenitors

first: Kevin

last: Lebrigand

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Elongin functions as a loading factor for Mediator at ATF6α-regulated ER stress response genes

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research


title: Bulk RNA sequencing of TCM, TEM, and TRM  from CD8+CD44+GP33+ T cells after LCMV infection

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

summary: During acute infections, CD8+ T cells form various memory subpopulations to provide long-lasting protection against reinfection. Central memory (TCM), Effector memory (TEM), and long-lived effector (LLE) cells are circulating memory populations with distinct plasticity, migration patterns, and effector functions. Tissue-resident memory (TRM) cells permanently reside in the frontline sites of pathogen entry and provide tissue-specific protection upon reinfection. Here, using scRNA-seq and bulk RNA-seq, we examined the different and shared transcriptomes and regulators of TRMs with other circulating memory populations. Furthermore, we identified heterogeneity within the TRM pool from small intestine and novel transcriptional regulators that may control the phenotypic and functional heterogeneity of TRM cells during acute infection. Our findings provide a resource for future studies to identify novel pathways for enhancing vaccination and immunotherapeutic approaches.

overall_design: There are three CD8 memory groups, TEM, TCM, and TRM. CD8+CD44+GP33+ cells were sorted from LCMV infected mice at day 30 post infection. TEM and TCM cells are sorted from spleen, seperated by CD62L. TRM  cells are sorted from intraepithelial lymphocytes from small intestine. There are 2-3 replicates for each cell group.

first: Yao


title: RNA-sequencing of Atf4fl/fl versus LAtf4KO mouse livers with fasting and physiological feeding

city: Boston

first: VICTOR

last: BARRERA BURGOS

state: Massachusetts

address: Landmark 401 Park Drive 3 East

department: Biostatistics

institute: Harvard School of Public Health

summary:
Purpose: To define the ATF4-dependent transciptional response with feeding in the liver
Male mice, 8 weeks of age were subjected to a 12h fast in the light cycle and fed a high carbohydrate diet for 6h in the dark cycle

overall_design: Liver mRNA profiles in Atf4fl/fl and Liver-specific Atf4 knockout mice with fasting and physiological feeding

first: Brendan

last: Manning

first: Vanessa

last: Byles

first: Victor

last: Barrera

first: Shannan

last: Ho Sui


title: Expression data from dissected postnatal 0 (P0) Meg2 (protein-tyrosine phosphatase non-receptor type 9, Ptpn9) knockout and wild-type mouse retinae.

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

summary: In our dataset, we included the expression data obtained from P0 dissected Meg2 knockout and wild-type mouse retinae. Most interestingly, we observed a dysregulation of several candidate genes known to be differentially expressed in response to retinal/glaucomatous neurodegeneration, which includes genes related to apoptosis, excitotoxicity, immune activation, neurotrophic signaling, oxidative stress and loss of synaptic integrity. These data indicate the importance and functional relevance of the protein tyrosine phosphatase Meg2 in retinal integrity and disease.

overall_design: In total 6 samples from 3 control wild-type and 3 Meg2 knockout mice were analyzed.

first: Andreas

last: Faissner

first: Jacqueline

last: Reinhard


title: Deciphering the cell-specific role of Arabidopsis Argonaute 3 [smallRNA-Seq]

city: Zurich

first: Antonin

last: Marchais

address: Universitatstrasse 2

department: Department of Biology

institute: ETHZ

summary: ARGONAUTE (AGO) proteins are the major effectors of RNA silencing. In Arabidopsis, loading of 21-22-nt long small RNAs into AGOs results in post-transcriptional gene silencing (PTGS) by mRNA cleavage and/or translational repression. On the other hand, loading of 24-nt sRNAs results in transcriptional gene silencing (TGS) by RNA directed DNA methylation (RdDM). The Arabidopsis genome encodes 10 AGOs, which are known, for most, to belong to either pathway. Here we characterized the cell specific role of Arabidopsis AGO3. It is specifically expressed in tissue close to vascular termination and strongly accumulates in chalazal seed integuments. AGO3 encodes a functional AGO able to bind sRNAs with a preference for 24nt in length with a 5’ nucleotide bias for Adenosine. Down-regulation of AGO3 affects gene expression in siliques and its expression is strongly induced in the plant vasculature upon proteasome inhibition. Our results suggest that AGO3 might act to regulate gene expression by a novel RNA silencing pathway involving 24nt sRNA-directed PTGS.

overall_design: small RNAs co-Immunoprecipitating with  FLAG AGO3 protein from siliques and, after a SyrginolinA treatment,  from plantlets  were sequenced using Illumina platform.

first: Pauline

last: Jullien

first: Nathan

last: Pumplin

first: Clement

last: Chevalier

first: Gregory

last: Schott

first: Caroline

last: Otto

first: Olivier

last: Voinnet


title: Deciphering the cell-specific role of Arabidopsis Argonaute 3 [RNA-seq]

overall_design: Transcriptome of Arabidopsis Col-0 Wt and ago3-3 mutant siliques were generated by stranded paired-end deep sequencing, in duplicate, using Illumina HiSeq 2000


title: Deciphering the cell-specific role of Arabidopsis Argonaute 3


title: Reduction of excessive Kcnn2 activity ameliorates learning disability in the mouse model of Fetal Alcohol Spectrum Disorders

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Learning disabilities are hallmarks of congenital conditions caused by prenatal exposure to harmful agents. This is particularly true for patients suffering from Fetal Alcohol Spectrum Disorders (FASD) who exhibit a wide range of cognitive deficiencies including impaired motor skill development. While these effects have been well characterized, the molecular effects that bring about these behavioral consequences remain to be determined. We have previously found that the acute molecular responses to alcohol in the embryonic brain are stochastic, varying among neural progenitor cells. However, the pathophysiological consequences stemming from these heterogeneous responses remain unknown. Here we show that acute responses to alcohol in progenitor cells lead to altered gene expression in their descendant neurons at the single-cell level. Among the altered genes, we found that an increase of the calcium-activated potassium channel Kcnn2 in subset neurons in the motor cortex correlates with motor skill learning deficits in the mouse model of FASD. We further show that postnatal blocking of Kcnn2 improves these learning deficits. These results propose Kcnn2 blockers as a novel intervention for learning disabilities in FASD and possibly for other neurocognitive conditions.

overall_design: Total 28 samples were analyzed; 7, 15, and 5 replicates each for reporter-EtOH, reporter+EtOH, and reporter-PBS groups, respectively.

first: Shahid

last: Mohammad

first: Stephen

last: Page

first: Li

last: Wang

first: Seiji

last: Ishii

first: Peijun

last: Li

first: Toru

last: Sasaki

first: Aiesha

last: Basha

first: Anna

last: Salzberg

first: Zenaide

last: Quezado

first: Fumiaki

last: Imamura

first: Hirotaka

last: Nishi

first: Keiichi

last: Isaka

first: Joshua

last: Corbin

first: Judy

last: Liu

middle: I

last: Kawasawa

first: Masaaki

last: Torii

first: Kazue

last: Hashimoto-Torii


title: Cell-to-cell heterogeneity of phosphate gene expression in yeast is controlled by alternative transcription, 14-3-3 and Spl2

status: Public on Aug 29 2021

city: Leiden

first: Paul

last: van Heusden

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: Leiden University

summary: We investigated the effect of deletion of BMH1, SPL2 and RRP6 on gene expression in the yeast Saccharomyces cerevisiae. In addition, the effect of 60 min phosphate starvation was studied in the SPL2 deletion mutant as well as in the parental strain BY4741. Finally, the effect of deletion of specific parts of the SPL2 promoter was investigated. Transcriptome analysis was performed by strand-specific RNAseq.

overall_design: For BY4741 three independent cultures cultivated at 7.2 mM potassium phosphate and three independent cultures cultivated without phosphate were used. For spl2Δ three independent cultures cultivated at 7.2 mM potassium phosphate and two independent cultures cultivated without phosphate were used. For bmh1Δ one culture cultivated at 7.2 mM potassium phosphate was used. For rrp6Δ RNAseq was done in a separate experiment including two independent cultures of rr6Δ and one culture of BY4741 cultivated at 7.2 mM potassium phosphate. For studying the effect of deletion of block P of the SPL2 promoter a separate experiment was conducted with one culture of BY4741 and one culture of BY4741 ΔP cultivated at 7.2 mM potassium phosphate.

first: G


title: PROPER-seq (PROtein Protein intERaction sequencing)

city: La Jolla

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Drive, MC 0412

department: Department of Bioengineering

institute: University of California, San Diego

summary: To reveal protein-protein interactions at transcriptomic scale by sequencing

overall_design: PROPER-seq converts the input transcriptome into a library of RNA-barcoded proteins and subsequently reverse transcribes and ligates the two RNA barcodes of each PPI to yield a chimeric DNA sequence. This approach enables simultaneous conversion of many PPIs into chimeric DNA sequences and subsequent decoding of the PPIs by sequencing these chimeric sequences

first: Kara

last: Johnson

first: Zhijie

last: Qi

first: Xueyi

last: Wan

first: Chienju

last: Chen

first: Xingzhao

last: Wen

first: Zhangmin

last: Yan


title: Genome-wide maps of TLR3 activated human keratinocytes compared with control human keratinocytes

city: Dublin

first: Jianghui

last: Meng

address: Glasnevin Avenue

institute: Dublin City University

summary: In the present study, RNA sequencing of 6 human keratinocytes cell samples was performed. They are 3 samples of Poly (I:C)-treated cells, and 3 samples from un-treated control  cells,  from 3 different human donors. Total RNA was isolated from the cell samples and one RNA sequencing library was prepared from the 6 RNA samples with the Illumina TruSeq Stranded mRNA HT technolog. This approach uses fragmentation, a poly-T oligo pulldown and sequencing adaptor ligation. RNA sequencing was performed on the Illumina NextSeq500 next generation sequencing system and its high output mode with 1x75 bp single-end red chemistry.

overall_design: Examination of TLR3 activation in human primary keratinocytes on the regulation of gene expression.

first: Jiafu

last: Wang

first: Martin

last: Steinhoff


title: Bub1 and CENP-U redundantly recruit Plk1 to stabilize kinetochore-microtubule attachments and ensure accurate chromosome segregation

city: Hangzhou

first: zhang

last: miao

address: Zhejiang Hangzhou Yuhangtang road

institute: Zhejiang University

summary: Bub1 is required for the kinetochore/centromere localization of two essential mitotic kinases Plk1 and Aurora B. Surprisingly, stable depletion of Bub1 by ~95% in human cells marginally affects whole chromosome segregation fidelity. We show that CENP-U, which is recruited to kinetochores by the CENP-P and CENP-Q subunits of the CENP-O complex, is required to prevent chromosome mis-segregation in Bub1-depleted cells. Mechanistically, Bub1 and CENP-U redundantly recruit Plk1 to kinetochores to stabilize kinetochore-microtubule attachments, thereby ensuring accurate chromosome segregation. Furthermore, unlike its budding yeast homolog, the CENP-O complex does not regulate centromeric localization of Aurora B. Consistently, depletion of Bub1 or CENP-U sensitizes cells to the inhibition of Plk1 but not Aurora B kinase activity. Taken together, our findings provide mechanistic insight into the regulation of kinetochore function, which may have implications for targeted treatment of cancer cells with mutations perturbing kinetochore recruitment of Plk1 by Bub1 or the CENP-O complex.

overall_design: RNA-seq analysis of HeLa and Bub1-depleted cells, B=Bub1-depleted clone 2B6, C=Bub1-depleted clone 2C1, H=Control HeLa cells. H1, H2, H3 are replicates, B1, B2, B3 are replicates, C1, C2, C3 are replicates.

first: Qinfu

first: Miao

last: Zhang

first: Xuan

last: Pan

first: Xueying

last: Yuan


title: Oxidized Low-Density Lipoprotein drives dysfunction of the liver lymphatic system

status: Public on Aug 28 2021

city: Aurora

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

summary: Single-cell RNA-sequencing revealed that the transcriptional profile of LECs from HFHC livers was consistent with changes in the LEC transcriptome that reflect both proliferation and a potential de-differentiation of liver LECs in the context of disease which may impact their functions, such as permeability and metabolism.

overall_design: Liver stromal cells were harvested from mice fed either control or high fat, high cholesterol diet, flow sorted to enrich for endothelial cell populations  and subjected to single-cell RNA-seq.

first: Matthew

last: Burchill

first: Rachel

last: McMahan

first: Beth

last: Jirón Tamburini


title: Comprehensive analysis of adrenocortical steroidogenesis in human and mouse

first: Neelanjan

last: Mukherjee

department: BMG/RBI

institute: University of Colorado School of Medicine

summary: We analyze gene regulatory mechanisms involved in adrenocortical steroidogenesis using assays to measure RNA expression, synthesis, decay, processing, translation and miRNA expression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Metabolic labeling, ribosome profiling and small RNA-sequencing was performed on human H295R adrenocortical cell lines with and without treatment with angiotensin or forskolin. RNA-seq was performed on adrenal glands of p15 c57bl/6 mice.


title: CD11c+ Expression Associates with IFN-λ Responsiveness in Human B cells with clinical implications for SLE

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

summary: Type I interferon (IFN), namely IFN- α, and B cell aberrations are long recognized in systemic lupus erythematosus (SLE) pathogenesis. Type I IFN receptor blockade has undergone clinical trials in SLE with varying degrees of success. Type III IFN (IFN-λ) produce a gene signature currently indistinguishable from that of type I in responsive cell types. IFN-λ are not blocked by type I IFN receptor blockade as they utilize a unique receptor (IFNLR1). Type III IFN are appreciated to have an important role in viral infection at epithelial barriers where IFNLR1 is strongly expressed.  The effects of IFN-λ on immune cells remain understudied and are different between human and murine models.  We have previously shown that human B cells can transcribe type I IFN genes after IFN-λ treatment including those associated with SLE. We have found that IFN-λ is detected in the serum of human SLE patients and correlates with IgD- CD27- CD21- CD24- (DN2) B cells, a compartment which contains CD11c+ age/autoimmunity B cells (ABC).  ABC are a target of interest as recent studies suggest they are poised for plasma cell differentiation and enriched in autoreactivity and thus have the potential to contribute to SLE pathogenesis. Results: Naïve and DN cells display a prominent type I IFN gene expression profile in SLE. Transcript for type I, type II, and type III IFN receptors (IFNAR1, IFNAR2, IFNGR1, IFNGR2, IFNLR1, and IL10RB) are detected in HD and SLE B cells.  CD11c+ CD21- frequency increased in DN compared to naïve B cells for SLE and HD (both p< 0.001).  The mean and range of CD11c+ CD21- frequency was higher in SLE DN (30.7± 9.5%, mean±SEM; range 4.8-74.7%) compared to HD DN (7.6%±1.0%,3.6-9.4%). Increased IFNLR1 transcript correlated with CD11c+ CD21- B cell expansion (r2=0.922, p<0.0001). Increased pSTAT1 after IFN-α2 treatment is found in monocytes, T cells, and B cells but only in the B cells after IFN-λ1 treatment.  Naïve, DN, switched, and unswitched memory HD B cells are responsive to type I and type III IFN, but demonstrated a higher pSTAT1 fold change with type I IFN treatment compared to type III IFN.  In all B cell subsets, CD11c+ cells had a higher pSTAT1 fold change after IFN-λ1 stimulation than did CD11c- B cells. In HD with well-defined populations of CD11c+ CD21- DN cells, pSTAT1 fold change for IFN-λ approached that of IFN-α2.  Conclusions:  All human B cell subsets defined by CD27 and IgD respond to IFN-α and IFN-λ, but those expressing CD11c+ have increased responsiveness to IFN-λ.  CD11c+ cells expand in SLE and associate with autoreactive plasma cell development.  Thus, the role of IFN-λ may take on increased clinical significance in the setting type I IFN receptor blockade.  These results suggest IFN-λ is an underappreciated driver of the IFN signature and B cell aberrations in SLE.

overall_design: Patients meeting 1997 ACR systemic lupus erythematosus classification criteria (n = 8) and healthy donors (HD, n = 5) had blood drawn under IRB-approved protocol. The transcriptome of sorted IgD+ CD27- naïve and IgD- CD27- (DN) B cells was measured by bulk RNA sequencing for differential expression and gene set enrichment analysis. Cell phenotype and STAT1 phosphorylation (pSTAT1) in IFN-α2 and IFN-λ1 treated PBMC was measured by flow cytometry (n =10).

first: Jennifer

last: Barnas

last: Anolik

first: John

last: Looney

first: Nida

last: Meednu

first: Andrew

last: McDavid


title: Transcriptome analysis of CHD8 ko mice

city: safed

first: Evan

last: Elliott

state: safed

address: 8 henrietta szold

institute: Bar Ilan University

summary: Autism Spectrum Disorders includes several behavioral phenotypes in addition to other comorbid conditions. One of the strongest comorbidities in Autism is gastrointestinal issues. Gastrointestinal issues are also prevalent in individuals with mutations in CHD8, which is one of the top autism-related genes. However, the relationship between autism related genes, such as CHD8, gastrointestinal function, and autism related behaviors are yet very unclear. In this study our goal is to explore the molecular mechanism and connection between CHD8 KO and gastrointestinal problems.

overall_design: RNA sequencing between wild type and CHD8+/- mice

first: Ipsita

last: Chatterjee


title: Antigen-receptor stimulation drives purifying selection against pathogenic mitochondrial DNA variants that dysregulate lymphocyte responses

status: Public on Aug 27 2021

city: Stockholm

first: Joanna

last: Rorbach

state: Not Applicable (Outside of US and Canada)

address: Solnavägen 9, 9d 171 77 Stockholm, Sweden

department: Department of Medical Biochemistry and Biophysics

country: Sweden

institute: karolinska institute

summary: Metabolic transcriptomic signatures of CD8+ T cells during timecourse activation were profiled in CD8 T cells isolated from 4 WT and 4 C5024T mice. Mice were age (2-month-old) and sex matched. Briefly, for each mouse, freshly purified (negative selection) splenic naïve CD8+ T cells were seeded at a density of 200,000 cells/well and activated using a 1:1 (bead:cell) ratio with Dynabeads Mouse T-Activator CD3/CD28 for 6 and 96 hr at 37oC (5% CO2) . 200,000 ex vivo purify ed naïve CD8+ T cells were collected for baseline (0 hr) measurement.

overall_design: 4wt and 4 C5024T mice,from each mice, sub-divided into three groups: naive CD8 T cell, CD8 T cell post_6h activation, CD8 T cell_post 96h activation.

first: Jingdian

first: Xaquin

last: Castro Dopico


title: MiRNA sequencing revealed differentially expressed exosomes miRNAs in PDE of patients with peritoneal ultrafiltration failure

city: Huzhou

first: weifei

last: wu

state: Zhejiang Province

address: 1588, 3rd Ring North Road, Wuxing District

institute: Huzhou Hospital, Zhejiang University School of Medicine

summary: There are differential expressions of exosomal miRNAs in PDE of patients with peritoneal ultrafiltration failure. It may be related to the occurrence of peritoneal ultrafiltration failure by regulating the process of peritoneal fibrosis such as inflammation, angiogenesis, and EMT.

overall_design: Include 6 samples, 3 are exosomes of type I peritoneal ultrafiltration failure, another 3 are exosomes of controls with stable peritoneal function.

first: Weifei

last: Wu

first: Xu

first: Zhiqun

last: Cheng

first: Minhui

last: LU


title: The small RNA sequencing data of EcoHIV-infected mouse brain tissue derived extracellular vesicles

city: Baltimore

first: XIAOLEI

last: ZHU

state: MD

address: 417 old trail rd

institute: JHU

summary: Given the nefarious role that Extracellular vesicles (EVs) can play in disease pathogenesis, there is a growing interest in examining the contents of EVs in many disorders, including depression, HIV, and HIV-Associated Neurocognitive Disorder (HAND). EVs are particularly enriched with miRNA, and the nervous system expresses approximately 70% of all miRNA. miRNA typically regulate gene expression via degrading or suppressing mRNA translation, and these small non-coding RNAs, which are thought to be shuttled between cells via EVs, have been implicated in a host of diseases and conditions, including depression and cognitive decline. To our knowledge, however, this is the first study to examine brain-derived (bd) EV miRNA content in a preclinical model of HIV-associated CI and depression. We report 4 miRNAs, including miR-429-3p, miR-200c-3p, miR-183-5p, and miR-200b-3p, that are significantly upregulated in bdEVs of EcoHIV-infected mice and normalized by novel treatment.

overall_design: People living with HIV (PLWHIV) have significantly higher rates of cognitive impairment (CI) and major depressive disorder (MDD) versus the general population. The enzyme neutral sphingomyelinase 2 (nSMase2) is involved in the biogenesis of ceramide and extracellular vesicles (EVs), both of which are dysregulated in PLWHIV, CI, and MDD. Here we evaluated EcoHIV-infected mice for behavioral abnormalities relevant to depression and cognition deficits, and assessed the behavioral and biochemical effects of nSMase2 inhibition. RNA was extracted from EVs separated from the prefrontal cortex (PFC) or hippocampus (HPC) of control and EcoHIV-infected mice with/without nsMase2 inbitor treatment. Given the relatively low yield of EVs, samples were pooled from 6-8 mice for small RNA sequencing.

first: Xiaolei

last: Zhu

first: Yiyao

last: Huang

first: Kenneth

middle: W

last: Witwer

first: Kristen

last: Hollinger

first: Tanina

last: Arab

first: Andrey

last: Turchinovich


title: Inappropriate use of antibiotics exacerbates inflammation through OMVs-induced pyroptosis in multidrug-resistant Klebsiella pneumoniae infection

city: Kunming

first: Yanbing

last: Ma

state: Yunnan

address: NO.935 Jiaoling Road

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: The inappropriate use of antibiotics is a severe public health problem worldwide, contributing to the emergence of multidrug-resistant (MDR) bacteria. To explore the possible impacts of the inappropriate use of antibiotics on the immune system, we use Klebsiella pneumoniae (K. pneumoniae) infection as an example and show that imipenem increases the mortality of mice infected by MDR K. pneumoniae. Further studies demonstrate that imipenem enhances the secretion of outer membrane vesicles (OMVs) with significantly elevated presentation of GroEL, which promotes the phagocytosis of OMVs by macrophages that depends on the interaction between GroEL and its receptor LOX-1. OMVs cause the pyroptosis of macrophages and the release of proinflammatory cytokines, which contribute to exacerbated inflammatory responses. We propose that the inappropriate use of antibiotics in the cases of infection by MDR bacteria such as K. pneumoniae might cause damaging inflammatory responses, which underlines the pernicious effects of inappropriate use of antibiotic.

overall_design: bacterial transcriptional profile with and without treatment with imipenem of Klebsiella pneumoniae

first: Chao

last: Ye

first: Weiwei

first: Weiran

last: Li


title: The matricellular protein WISP2 is an endogenous inhibitor of collagen linearization and cancer metastasis

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

institute: St Jude Children's Research Hospital

summary: Collagen linearization leads to cancer metastasis and poor prognosis but there are no therapies to target it. In addition to cell-generated mechanical forces, collagen linearization is triggered by the interaction of collagen with WISP1 (CCN4), a TGFb1-induced factor secreted by cancer cells. However, it remains unknown how WISP1 is physiologically regulated and whether it could be targeted to prevent collagen linearization. Here, we show that WISP2 (CCN5), a secreted factor downregulated in tumors, is an endogenous inhibitor of type I collagen (Col I) linearization. Mechanistically, WISP2 prevents WISP1 binding to Col I, thereby inhibiting WISP1-induced Col I linearization. Consequently, restoration of WISP2 via overexpression in tumor cells or via treatments with recombinant WISP2 impairs WISP1-induced or TGFb1-induced cancer cell invasion and spontaneous metastasis in vivo. Overall, this study uncovers WISP2 as an endogenous competitive inhibitor of WISP1 and reveals that collagen linearization is controlled by secreted factors with antagonistic functions.

overall_design: Here 3 samples of 4T1 cells, a murine breast cancer cell line, were transformed such that WISP2 was over expressed.  These samples wrre compared to 4T1 controls transformed with an empty vector: GSM3018746, GSM3018748, and GSM3018749 in other analyses not presented here.

first: Jagadeesh

last: Janjanam

first: Glendin

last: Pano

first: Ruishan

last: Wang

first: Hannah

last: Breeze-Jones

first: Eleanor

last: Baker

first: Cecile

last: Garcin

first: Georgia

last: Clayton

first: Myriam

last: Labelle


title: Expression data of HNSCC cell lines in normoxia and hypoxia

city: Linköping

first: Emilia

last: Wiechec

address: Sandbäcksgatan 7

department: Biomedical and Clinical Sciences

institute: Linköping University

summary:
Hypoxia has been linked to increased treatment resistance in many solid tumors, including head and neck squamous cell carcinoma (HNSCC). We aim to identify genes involved in hypoxia-mediated response to radiotherapy in HNSCC.
We used microarrays to investigate the influence of hypoxia on the global gene expression in HNSCC.

overall_design: HNSCC cells ( LK0858, LK0863, UT-SCC-14) were grown in normoxic (21% O2) and hypoxic (1% O2) conditions and thereafter were selected  for RNA extraction and hybridization on Affymetrix microarrays.

first: Wiechec

last: Emilia

first: Ashfaq

last: Ali

first: Roberg

last: Karin


title: Histone acetyl transferase (HAT) and APSES TF of Aspergillus fumigatus

city: Daejeon

first: Kwang-Soo

last: Shin

department: Life Science

country: South Korea

institute: Daejeon University

summary: Transcriptome analysis of deletion mutant which coding HAT and APSES TF compared to wild type by NGS

overall_design: Examination of mutant and wild type transcriptome


title: Halting the FGF/FGFR axis leads to anti-tumor activity in Waldenström’s Macroglobulinemia by silencing MYD88

city: Brescia

first: Aldo

middle: Maria

last: Roccaro

state: BS

address: P.le Spedali Civili di Brescia, n. 1

country: Italy

institute: ASST Spedali Civili di Brescia

summary:
The human fibroblast growth factor/fibroblast growth factor-receptor (FGF/FGFR) axis deregulation is largely involved in supporting the pathogenesis of hematologic malignancies, including Waldenström’s Macroglobulinemia (WM). WM is still an incurable disease, and patients succumb due to disease progression. Therefore, novel therapeutics designed to specifically target deregulated signaling pathways in WM are required. We aimed to investigate the role of FGF/FGFR blocking system in WM by using a pan-FGF trap molecule (NSC12).
Wide-transcriptome profiling confirmed inhibition of FGFR-signaling in NSC12-treated WM cells; unveiling a significant inhibition of Myd88 also confirmed at protein level. Importantly, the  NSC12-dependent silencing of Myd88 was functionally active, as it led to inhibition of Myd88-driven pathways, such as BTK and SYK, as well as the Myd88-downstream target HCK. Of note, both canonical and non-canonical NFB cascades were down-regulated in WM cells upon NSC12 treatment. Functional sequelae exerted by NSC12 in WM cells were studied, demonstrating significant inhibition of WM cell growth, induction of WM cell apoptosis, halting MAPK, JAK/STAT3 and PI3K-Akt pathways. Importantly, NSC12 exerted an anti-WM effect even in the presence of bone marrow microenvironment, both in vitro and in vivo. Our studies provide the evidence for using NSC12 as a specific FGF/FGFR system inhibitor, thus representing a novel therapeutic strategy in WM.

overall_design: BCWM.1 and MWCL.1 cell lines were analyzed after treatment with NSC12 (6µM) for 12 hours in comparison to untreated cells. All experiments were performed in triplicates for each condition.

first: Antonio

last: Sacco

first: Cinzia

last: Federico

first: Arianna

last: Giacomini

last: Caprio

first: Federica

last: Maccarinelli

first: Katia

last: Todoerti

first: Vanessa

last: Favasuli

first: Antonella

last: Anastasia

first: Marina

last: Motta

first: Giuseppe

last: Rossi

first: Nicole

last: Bozza

first: Riccardo

last: Castelli

first: Antonino

last: Neri

first: Roberto

last: Ronca

first: Chiara

last: Cattaneo

first: Alessandra

last: Tucci

first: Marco

last: Mor

last: Presta


title: MUSASHI-2 RNA binding protein confers resistance to an epidermal growth factor receptor-tyrosine kinase inhibitor Osimertinib in lung adenocarcinoma

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

summary: Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are effective in non-small cell lung cancer (NSCLC) patients harboring EGFR mutations. However, due to the acquired resistance to EGFR-TKIs, even third generation Osimertinib, the patients suffer poor prognosis. The resistance mechanisms are still not fully understood. Here, we demonstrate that increased expression of MUSASHI-2 (MSI2), an RNA binding protein, is novel mechanisms for resistance to EGFR-TKIs. We found that after long-exposure of gefitinib, the first generation EGFR-TKI, lung cancer cells harboring the EGFR-TKI-sensitive mutations became resistant to not only gefitinib but also Osimertinib. Although other mutations in EGFR were not found, expression levels of Nanog, a stemness core protein, and activities of aldehyde dehydrogenase (ALDH) were increased, suggesting that cancer stem-like properties were increased. Transcriptome analysis revealed that MSI2 was among the top list of the stemness-related genes upregulated in the EGFR-TKI-resistant cells. Knockdown of MSI2 reduced cancer stem-like properties, including expression levels of Nanog a core stemness factor. We demonstrate that knockdown of MSI2 restored sensitivity to Osimertinib or gefitinib in the EGFR-TKI-resistant cells to the similar levels of the parental cells in vitro. RNA immunoprecipitation (RIP) assay revealed that antibodies against MSI2 bound to Nanog mRNA, suggesting that MSI2 increases Nanog expression by binding to Nanog mRNA. Moreover, overexpression of MSI2 or Nanog conferred resistance to Osimertinib or gefitinib in parental cells. Finally, knockdown of MSI2 greatly increased sensitivity to Osimertinib in vivo. Collectively, our findings provide proof-of-principle that targeting MSI2-Nanog axis in combination with EGFR-TKIs would effectively prevent emergence of acquired resistance.

overall_design: Comaprison in ALDH-high cell populations between PC9 cells and PC9M2 cells.There are four biological replicates for each conditions.

first: Reheman

last: Yiming

first: Yasuto

last: Takeuchi

first: Tatsunori

last: Nishimura

first: Li

last: Mengjiao

first: Yuming

last: Wang

first: Makiko

last: Meguro-Horike

first: Asuka

last: Nakata

first: Noriko

last: Gotoh


title: Distruption of DMRT1 induces feminization in Chicken

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

institute: Seoul National University

summary: RNA-sequencing data to inversigate the effects of DMRT1-distruption at E6 and 1W time points in male and female chickens.

overall_design: This RNA-sequencing data was generated under three experimental factors such as Time, Sex, and DMRT(-). Since each condition has two levels and 3 biological replications, a total of 24 sampels were paired-end sequenced.

first: Jae

last: Han

first: Hong

last: Lee


title: A unique cell wall synthetic response evoked by glucosamine determines pathogenicity-associated fungal cellular differentiation

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

country: China

institute: the institute of microbiology chinese academy of sciences

summary: The yeast-to-hypha transition is tightly associated with pathogenicity in many human pathogenic fungi, such as the model fungal pathogen Cryptococcus neoformans, which is responsible for approximately 180,000 deaths annually. In this pathogen, the yeast-to-hypha transition can be initiated by distinct stimuli: mating stimulation or glucosamine (GlcN), the monomer of cell wall chitosan. However, it remains poorly understood how the signal specificity for Cryptococcus morphological transition by disparate stimuli is ensured. Here, by integrating temporal expression signature analysis and phenome-based clustering evaluation, we demonstrate that GlcN specifically triggers a unique cellular response, which acts as a critical determinant underlying the activation of GlcN-induced filamentation (GIF). This cellular response is defined by an unusually hyperactive cell wall synthesis that is highly ATP-consuming. A novel cell surface protein Gis1 was identified as the indicator molecule for the GlcN-induced cell wall response. The Mpk1-directed cell wall pathway critically bridges global cell wall gene induction and intracellular ATP supply, ensuring the Gis1-dependent cell wall response and the stimulus specificity of GIF. We further reveal that the ability of Mpk1 to coordinate the cell wall response and GIF activation is conserved in different Cryptococcus pathogens. Phosphoproteomics-based profiling together with genetic and phenotypic analysis revealed that the Mpk1 kinase mediates the regulatory specificity of GIF through a coordinated downstream regulatory network centered on Skn7 and Crz1. Overall, our findings discover an unprecedented and conserved cell wall biosynthesis-dependent fungal differentiation commitment mechanism, which enables the signal specificity of pathogenicity-related dimorphism induced by GlcN in Cryptococcus pathogens.

overall_design: 29 samples contain wildtype at seven time points with 3 repeats and wildtype, crz1Δ, mpk1Δ, znf2Δ at one time point with two repeats.

first: Pengjie

last: Hu

first: Hao

last: Ding

first: Lan

last: Shen

first: Guangjun

last: He

first: Linqi


title: TfR1 extensively regulates the expression of genes associated with ion transport and immunity

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: The transferrin receptor 1 (TfR1), encoded by TFRC gene, is the gatekeeper of cellular iron uptake for cells. A variety of molecular mechanisms are at work to tightly regulate TfR1 expression, and abnormal TfR1 expression was associated with diseases. In the current study, to figure out the regulation pattern of TfR1, we cloned and overexpressed human TFRC gene in HeLa cells. RNA-sequencing (RNA-seq) was used to analyze the global transcript level on overexpression-treated (OE) and normal control (NC) cell samples. 1669 differentially expressed genes (DEGs) were identified between OE and NC, and Gene ontology (GO) analysis for DEGs were carried out. It was found that lots of DEGs were associated with ion transmembrane transport and immunity. Moreover, the network was constructed on basis of DEGs regulating ion transport and immunity, the results revealed that TFRC was the node gene of the network, further suggesting that precisely controlled TfR1 expression might be not only essential for iron homeostasis, but also globally important for cell physiology, including ion transport and immunity.

overall_design: To explore the regulation pattern of TfR1, we cloned and overexpressed human TFRC in HeLa cells. Subsequently, RNA-sequencing (RNA-seq) was carried out in overexpression-treated (OE) and normal control (NC) cell samples, and the results indicated that TfR1-overexpression globally affect expression levels of numerous genes. A large number of differentially expressed genes (DEGs) were identified, and Gene ontology (GO) analysis revealed that these DEGs were associated with regulation of ion transmembrane transport, immunity and transcription, suggesting abnormal high expression level of TfR1 might globally disrupt the cell physiology through molecular mechanisms.

last: Huang


title: Astrocyte-selective transduction with AAV5 viral vector does not exacerbate astrogliosis or alter tissue immune responses following spinal injury

status: Public on Aug 26 2021

city: Auckland

first: Connor

middle: Andrew

last: Clemett

state: Auckland

address: 85 Park Rd

department: Anatomy and Medical Imaging

country: New Zealand

institute: University of Auckland

summary:
Following contusive spinal injury astrocytes undergo inflammatory activation and proliferation in a process known as astrogliosis. Reactive astrocytes are attractive therapeutic targets as they sit central to many of the immune recruitment, injury response, and tissue healing processes of the spinal cord. However, methods of targeted expression of exogenous therapeutic genes within astrocytes must be validated to not alter the normal immunological involvement of astrocytes.
To investigate the effect of transgene expression within astrocytes upon the immunological state of the contused cord, we injected the astrocyte-selective AAV5-GfaABC1D-dYFP reporter vector into an animal model of moderate contusive spinal cord injury. Bulk RNA microarrays were used to assess transcriptomic changes of the perilesional tissue.

overall_design: Adult female Sprague-Dawley rats (220-250 g) underwent surgical T10 laminectomy and moderate contusive injury (175 kDyn) by an Infinite Horizons impactor. Treatment groups were acutely administered the AAV5-GfaABC1D-dYFP reporter vector at the time of surgery by stereotaxic microinjection. Following recovery, at 7- and 28-days post-injury animals were euthanised and the spinal tissue taken for Clariom S Rat microarrays or fixed in paraformaldehyde (4%, pH7.4) for immunohistochemistry.

first: Barbara

last: Fackelmeier

first: Dahna

last: Fong

first: Alexandre

last: Mouravlev

first: Deborah

last: Young

first: Simon

last: O'Carroll


title: Small RNA sequencing Analysis of muscle and adipose in Chinese swamp buffalo

city: Xinyang

first: Yun

last: Ma

address: Shihe

institute: Xinyang Normal University

summary: Background: Intramuscular fat (IMF) content is an important index for beef quality. However, the genetics of IMF deposition is complex and still largely unclear, especially in buffalo. To identify miRNAs with potential regulatory role in lipid accumulated in muscle, we performed small RNA sequencing and identified miRNAs expressed in the longissimus dorsi muscle and back fat of Chinese buffalo, which provided vital information for further identification of miRNAs with potential regulatory role in the lipid accumulated in muscle. Results: Six small RNA libraries were constructed. A total of 66,128,645 and 70,974,347 raw reads were obtained from muscle and adipose groups, respectively. After filtering the adaptor and low quality reads, 60,765,257 and 67,327,095 clean reads were retained. In total, 721 miRNAs were identified.

overall_design: Three muscle samples and three adipose samples from Chinese swamp buffalo were collected from Benniu abattoir, a local slaughterhouse of Xinayang, P.R. China.

first: Jieping


title: Hepatocellular carcinoma: recurrence after liver transplantation and the primary cancer

city: Tianjin

first: Tao

last: Liu

address: 24 Fu-Kang Road, Nan-Kai District

department: First Central Hospital

institute: Nankai University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: Liver transplantation (LT) is an optimal treatment for a selected group of hepatocellular carcinoma (HCC) patients. However, about 10%-25% of LT cases develop post-transplant HCC recurrence, which drastically reduces the long-term survival of HCC patients. This study gives an analysis of the recurrent HCC after LT and the corresponding primary tumor. Results provide insight into the molecular mechanisms underlying post-LT HCC recurrence.

overall_design: Recurrent HCC tissue vs. primary HCC tissue from the same patient. Biological replicates: 2 cases.

first: Zhong-Yang


title: Genome-wide mapping of regulatory regions in seven domestic cat tissues [ChIP-seq]

city: College Station

first: William

middle: J

last: Murphy

state: TX

address: 4458 TAMU

department: Veterinary Integrative Biosciences

country: USA

institute: Texas A&M University

summary: Histone modifications and CTCF mark the locations of genomic regulatory regions -- including promoters, enhancers, and insulators -- and have not been previously annotated for the domestic cat genome. Understanding where non-coding sequence variants fall in relation to regulatory regions is vital for determining their impact on gene function and their ability to cause disease. The addition of replicated feline ChIP-seq data from multiple tissues will aid in interpretation of non-coding variants, furthering characterization of genetic diseases and genetic test development.

overall_design: Genomic DNA was extracted from seven tissues collected from adult male domestic shorthair cats (two biological replicates for each tissue), and ChIP-seq was performed with antibodies to three histone modifications (H3K27ac, H3K4me3, H3K27me3) and CTCF on all tissues. As a control, input DNA was sequenced for each tissue without the inclusion of an antibody. ENCODE quality metrics (NRF, PBC1, PBC2, NSC, and RSC) were calculated and included in the provided sample metadata.

first: Alexandra

middle: N

last: Myers


title: Placental trophoblast cells-derived exosomal microRNA-1290 promotes the interaction between endometrium and embryo by targeting LHX6

city: Hangzhou

first: Wang

last: zhengguang

address: Yuhangtang

institute: Zhejiang university

summary: Communication between the maternal uterus and the embryo is vital for a successful pregnancy. Exosomes, subtypes of extracellular vesicles comprising many bioactive factors regulate the early stages of pregnancy, specifically during embryo implantation. Nevertheless, the mechanism by which exosomal microRNAs (miRNAs) derived from placental trophoblasts regulate embryo implantation remains elusive. Herer, we isolated and identified exosomes derived from placental trophoblasts cells (HTR8/SVneo). Subsequently, we evaluated the loading miRNA in exosomes by small RNA sequencing. This study provides novel insights into the mechanism of trophoblasts cells-derived exosomes during embryo implantation.

overall_design: Three HTR8/Svneo cells and three HTR8/SVneo cells-derived exosomes samples were collected and sequenced using Illumina HiSeq. The miRNAs in cells and exosomes were mapped.

first: Shuang

last: Shi

first: Qiang

last: Tan

first: Zhengguang

last: Wang


title: Global gene expression profiling of M. tuberculosis H37Rv and the isogenic regX3-inactivated mutant (DregX3) grown in phosphate enriched or phosphate-limited medium

city: Kolkata

first: Manikuntala

last: Kundu

state: West Bengal

address: 93/1, Acharya Prafulla Chandra Road

institute: Bose Institute

summary: In order to understand the repertoire of genes regulated by RegX3, we performed microarray analysis of gene expression in M. tuberculosis (WT) or DregX3 grown in phosphate-enriched or phosphate limited medium. The differentially regulated genes provide insight into the role of RegX3 in gene regulation in Mtb.

overall_design: Gene expression profiling was performed in replicates for both the wild type and the isogenic DregX3 grown in phosphate enriched or phosphate limited conditions.

first: Amar

last: Chandra Mahatha

first: Joyoti

last: Basu

first: Sudipto

last: Saha


title: PPARg activation enhances myelination and neurological recovery in premature rabbits with intraventricular hemorrhage

city: BRONX

first: Praveen

last: Ballabh

state: New York

address: 1410 Pelham Parkway South

department: Pediatrics and Neuroscience

institute: ALBERT EINSTEIN COLLEGE OF MEDICINE

summary: We hypothesized that activation of PPARg would enhance myelination, reduce hydrocephalus, and promote neurological recovery in newborns with IVH. These hypotheses were tested in preterm rabbit model of IVH; autopsy brain samples from premature infants with and without IVH were analyzed. We found that IVH augmented PPARg expression in microglia of both preterm human infants and rabbit kits. The treatment with PPARg agonist or PPARg overexpression by adenovirus delivery further elevated PPARg levels in microglia, reduced pro-inflammatory cytokines, increased microglial phagocytosis, and improved oligodendrocyte progenitor cell (OPC) maturation in kits with IVH. Transcriptomic analyses of OPCs identified previously unrecognized PPARg-induced novel genes for purinergic signaling, cAMP generation, and antioxidant production, which would reprogram these progenitors toward promoting myelination. RNA-seq analyses of microglia revealed PPARg-triggered downregulation of several pro-inflammatory genes and transcripts having roles in Parkinson’s disease and amyotrophic lateral sclerosis, contributing to neurological recovery in kits with IVH. Accordingly, PPARg activation enhanced myelination and neurological function in kits with IVH.

overall_design: We performed two sets of RNA-seq: a) To address the effect of PPARg overexpression on microglial transcriptome, we performed a RNA-seq analysis on CD45Low/CD11b+ microglia isolated from the cerebral hemispheres of Ad-PPARg or Ad-GFP treated kits with IVH by FACS at D7; b) To determine the effect of PPARg overexpression on OPC transcriptome, we performed a RNA-seq analysis on O4+ OPC isolated from the cerebral hemispheres of Ad-PPARg and Ad-GFP treated preterm kits with IVH at D7.

first: Bokun

last: Cheng

first: Jinghang

last: Zhang

first: Xusheng


title: Genome-wide association study of RegX3 in M. tuberculosis (Mtb) grown under phosphate limited conditions

summary: In order to understand the role of the transcriptional regulator RegX3 in regulating gene expression under phosphate limitation, we performed chromatin immunoprecipitation with RegX3 antibody followed by next generation sequencing using the immunoprecipitate. We observed RegX3 binding at a number of loci including genes which were observed to be differentially regulated during growth in phosphate limited vs. phosphate enriched media, suggesting a global role of RegX3 in regulating gene expression under phosphate starvation.

overall_design: Genome-wide binding of RegX3 was analyzed by ChIP-seq  in M. tuberculosis grown under phosphate limiting conditions.


title: Downregulation of ARID1B, a tumor-suppressor in the WNT subgroup medulloblastoma, activates multiple oncogenic signaling pathways

city: Navi Mumbai

first: Neelam

middle: V

last: Shirsat

state: Maharashtra

address: Kharghar, Sector 21

department: Shirsat Lab

institute: Advanced Centre for Treatment, Research and Education in Cancer. Tata Memorial Centre

summary: About 85% of WNT subgroup medulloblastomas exhibit the loss of one copy of chromosome 6. Loss of function mutations were identified in the ARID1B gene located on chromosome 6 in WNT subgroup tumors suggesting tumor suppressor role for ARID1B in WNT medulloblastomas. The expression of ARID1B was downregulated in the medulloblastoma cell line Daoy using two independent shRNA sequences in a doxycycline-inducible lentiviral vector tet-pLKO-puro and the effect of its downregulation on the gene expression profile was studied by the RNA-seq analysis

overall_design: The expression of ARID1B was downregulated in a doxycycline-inducible manner in Daoy medulloblastoma cell line using the lentiviral vector tet-pLKO-puro. Total RNA was prepared from doxycycline-treated cells expressing the ARID1B shRNA and those expressing the vector alone  and the parental cells . Libraries were prepared from the polyA-enriched RNA fraction using the Illumina Truseq RNA library preparation kit and sequenced on the Illumina Hiseq 2500 platform

first: Akash

last: Deogharkar


title: mRNASeq of kidney, liver, and cerebellum of P195A/p150- and P195A/p150+ mice

city: Seattle

first: Megan

last: Maurano

state: Washington

address: 750 Republican St, Building E

department: Immunology

institute: University of Washington

summary: The goal of this experiement was to determine what transcriptional differences there are between P195A/p150- (sick) and P195A/p150+ (healthy) mice. Kidney, Liver, and Cerebellum were the most clearly affected on histology and qPCR for IFN. We found an IFN signature and ISR signature were both upregulated in P195A/p150- mice as compared to P195A/p150+ littermates.

overall_design: mRNA profiles of the liver, kidney, and cerebellum of 23 day old P195A/p150- and P195A/p150+ mice

middle: M

first: Daniel

middle: B

last: Stetson


title: Determination of transcript's polyA tail length in Wild-Type and Mov10 KO mouse ESCs.

city: Durham

first: Marcos

last: Morgan

address: 111 TW Alexander Dr

institute: NIEHS

summary: The RNA helicase MOV10 targets mRNAs to promote their decay. MOV10 can directly bind to N6-methyladenosine (m6A) nucleotides, the most prevalent type of mRNA internal modification in mammals. Here we investigate the mechanism by which MOV10 promotes decay by looking at changes in the polyA tail of its targets. PolyA tail length shortening is usually associated with transcript decay. However, we did not observe changes in the polyA profile for MOV10 targets in MOV10-depleted and Wild-Type controls. The observation was true for targeted transcripts containing the m6A modification and for targeted transcripts without the modification. We conclude that MOV10-mediated decay does not perturb the polyA tail dynamics of its targets in ESCs.

overall_design: Direct RNAseq between Wild-type and KO mouse ESCs

first: Brian

last: Papas

first: Yogesh

last: Kumar

first: Partha

middle: P

last: Das


title: MiR-592 activates the mTOR kinase, ERK1/ERK2 kinase signaling and imparts neuronal differentiation signature characteristic of Group 4 medulloblastoma

summary: The expression of miR-592 was found to reduce the malignant potential of Group 3 medulloblastoma cell lines, D283, D425 and HD-MB03.  RNA-seq analysis was carried out to identify genes differentially expressed upon miR-592 expression in the medulloblastoma cell lines. MiR-592 expression was found to upregulate mTOR and ERK1/ERK2 signaling and bring about neuronal differentiation in D283 and D425 cells. Transcriptome sequencing was also carried out on the RNA extracted from the polyclonal population of D283 and D425 expressing miR-592 as well as the  vector control population cells treated with rapamycin or U0126, a MAPK inhibitor to study if the mTOR signaling or MAPK signaling is instrumental in bringing about the neuronal differentiation.

overall_design: MiR-592 was expressed in a doxycycline-inducible manner in the medulloblastoma cell line using the lentiviral vector pTRIPZ. Total RNA was prepared from doxycycline-treated cells expressing miR-592 and those expressing the vector alone. Total RNA was also extracted from the doxycycline induced vector control and polyclonal population expressing miR-592, following treatment with mTOR signaling inhibitor  or MAPK signaling inhibitor. Libraries were prepared from the polyA-enriched RNA fraction using the Illumina Truseq RNA library preparation kit and sequenced on the Illumina Hiseq platform

first: Raikamal

last: Paul


title: Ab Initio Design of Amphipathic-Symmetric Peptides against SARS-CoV-2

first: Bocheng

last: Xu

state: China

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

institute: Zhejiang University

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes severe health crisis and huge socioeconomic upheaval internationally. This study proposes an ab initio design strategy to obtain antiviral peptides to against SARS-CoV-2 infection. The study employed database filtering technology to generate 7 amphipathic-symmetric peptides named DFTavPs with low cytotoxicity and random coil structure. Three DFTavPs promoted SARS-CoV-2 pseudoviruses infection and three DFTavPs inhibited virus infection, which are accompanied by up-regulation or down-regulation of SARS-CoV receptor angiotensin-converting enzyme 2 mRNA levels. Particularly, microRNA profiling showed that some differentially expressed microRNAs had potential to target key factors for cell entry of SARS-CoV-2. Furthermore, we explored the relationship of parameters and antiviral efficacy index (AEI). The results suggested that higher AEI of coronavirus was most likely to occur at mean amphipathic moment between 0.3 and 0.4. Automated machine learning was used to construct parameters-AEI regression models for various viruses. The Extra-Trees and CatBoost had a good predicting performance for AEI of coronavirus (R2=0.794 and Rpearson=0.897) and human immunodeficiency virus (R2=0.735 and Rpearson=0.859), respectively. Overall, this strategy is expected to efficiently obtain huge amounts of potential peptide drugs with anti-SARS-CoV-2 activity, and machine learning models could contribute to discovery of high antivirus-activity peptides.

overall_design: Examination of 2 antiviral peptides influence in 293T cells.

first: Xiao

last: Xiao

first: Xin

last: Zong


title: Acute depletion of CTCF rewires genome-wide chromatin accessibility

city: Memphis

first: Beisi

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

type: Methylation profiling by high throughput sequencing

summary: Accumulated data suggest that transcription factor CTCF is indispensable to define topologically associated domain (TAD) boundaries and to maintain intra-TAD chromatin loop structures. However, upon genome-wide acute depletion of CTCF, the discrepancy between global reduction of chromatin interactions and minimal alteration of transcription has been evidently observed. To understand CTCF’s direct role in chromatin accessibility and global transcriptional regulation, we have systematically integrated data collected from ATAC-seq, RNA-seq, whole genome bisulfite-seq, Cut&Run and HiC in a previously established CTCF-miniAID knock-in cell lines. Acute degradation of CTCF markedly rewires genome-wide chromatin accessibility but not DNA methylation. Differentially altered ATAC-seq peaks are highly associated with adjacent CTCF binding sites, supporting the direct link between CTCF occupancy and its surrounding chromatin accessibility. Increased ATAC-seq peaks upon CTCF loss are notably associated with enhanced transcription at promoter regions and insulator sites, while decreased ATAC-seq peaks are significantly enriched at DNA loops. Furthermore, using CTCF associated multi-Omics data we have established a combinatorial data analysis pipeline to discover novel CTCF mediated insulators in the genome, by which we have successfully identified 67 novel insulators at non-coding regions distal to promoters. Functional CRISPR interference (CRISPRi) unconstrained the repressive transcriptional regulation of target genes. In sum, using CTCF acute depletion cell model and multi-Omics analysis, we concluded that CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role for transcriptional regulation.

overall_design: Examination of chromatin accessibility by ATAC-seq and DNA methylation by WGBS in human SEM cell line in control and CTCF knockout by AID.

first: Shaela

last: Wright

first: Judith

last: Hyle

first: Yang

first: Ying

last: Shao

first: Yiping

last: Fan

first: Rui

last: Lu

first: Chunliang

last: Li


title: DNA methylation of a novel regulatory element within the tyrosine hydroxylase gene (TH) is dysregulated by chronic cocaine dependence in the human striatum

status: Public on Aug 25 2021

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

institute: McGill University

summary: This study investigates differences in DNA methylation that are associated with chronic cociane dependence in post-mortem nucleus accumbens tissue samples from human brain.  The data were generated with reduced representation bisulfite sequencing (RRBS) and compared to data generated in accumbens tissue from psychiatrically healthy controls.

overall_design: This study generated RRBS libraries from 25 males with a history of chronic cocaine dependence and cocaine toxicology at time of death, and 25 drug-naïve males.  Each sample was sequenced at least twice and raw reads were pooled for each individual. Raw data files represent pooled sequencing reads for each individual.


title: Effect of TAM_MK-8931 treatment on TAMs gene expression

city: Cleveland

first: Kui

last: Zhai

state: Ohio

address: 9620 Carnegie Ave n building, Cleveland, OH 44106

department: Cancer Biology

institute: CCF

summary: Glioblastoma (GBM), contains different tumor-associated macrophage (TAM) populations that can either promote tumor growth and therapeutic resistance (pTAMs) or have tumor suppressive properties (sTAMs), and thus reprograming pTAMs into sTAMs represents an attractive therapeutic strategy. By screening a collection of small molecule compounds we find that inhibition of the β-site amyloid precursor protein cleaving enzyme 1 (BACE1) by TAM_MK-8931 potently reprograms pTAMs into sTAMs and promotes macrophage phagocytosis of glioma cells; moreover, low-dose radiation markedly enhances TAM infiltration and synergizes with TAM_MK-8931 treatment to suppress malignant growth. BACE1 is preferentially expressed by pTAMs in human GBMs and is required for maintaining pTAM polarization through trans-IL-6-sIL-6R-STAT3 signaling. TAM_MK-8931 and other BACE1 inhibitors have been developed for Alzheimer's disease in clinical trials, and have been shown to be safe for humans, these could be potentially streamlined for cancer therapy. Collectively, this study offers a promising therapeutic approach to enhance macrophage-based therapy in GBM.

overall_design: Total TAMs (CD45+/Gr1-/CD11b+/DAPI-) were sorted from GBM xenografts through the fluorescence-activated cell sorting (FACS). Briefly, GBM xenografts were resected and mechanically dissociated and then digested in the HBSS containing 10 μg/mL DNase I (Sigma Aldrich) and 25 μg/mL Liberase (Roche) for 45 min at 37°C, mixed by pipetting every 10 min. After digestion, cell suspensions were passed through a 70 μm filter, put on ice, washed with cold PBS, and spun down (800 rpm) for 10 min at 4°C. Red blood cells in the samples were eliminated with red blood cell lysis buffer (BioLegend, 420301). The dissociated cells were re-suspended in the RPMI 1640 medium and blocked by the rat serum IgG (Santa Cruz, sc-2026) for 15 minutes before staining with specific antibodies for sorting. Antibodies used for FACS include: CD45 (Biolegend, 103127, Clone 30-F11), Gr1 (Biolegend, 108405, Clone RB6-8C5), and CD11b (Biolegend, 101207, clone M1/70). The sorted TAMs (CD45+/Gr1-/CD11b+/DAPI-) were then used for either RNA-seq analyses

first: Shideng

last: Bao


title: Effect of MK-8931 on GSC gene expression

summary: Glioblastoma (GBM), contains different tumor-associated macrophage (TAM) populations that can either promote tumor growth and therapeutic resistance (pTAMs) or have tumor suppressive properties (sTAMs), and thus reprograming pTAMs into sTAMs represents an attractive therapeutic strategy. By screening a collection of small molecule compounds we find that inhibition of the β-site amyloid precursor protein cleaving enzyme 1 (BACE1) by MK-8931 potently reprograms pTAMs into sTAMs and promotes macrophage phagocytosis of glioma cells; moreover, low-dose radiation markedly enhances TAM infiltration and synergizes with MK-8931 treatment to suppress malignant growth. BACE1 is preferentially expressed by pTAMs in human GBMs and is required for maintaining pTAM polarization through trans-IL-6-sIL-6R-STAT3 signaling. MK-8931 and other BACE1 inhibitors have been developed for Alzheimer's disease in clinical trials, and have been shown to be safe for humans, these could be potentially streamlined for cancer therapy. Collectively, this study offers a promising therapeutic approach to enhance macrophage-based therapy in GBM.

overall_design: Examination of gene expression inglioma stem cells treated by MK-8931 or control vehicle.